Spreads, arcs, and multiple wavelength codes

AbstractWe present several new families of multiple wavelength (2-dimensional) optical orthogonal codes (2D-OOCs) with ideal auto-correlation λa=0 (codes with at most one pulse per wavelength). We also provide a construction which yields multiple weight codes. All of our constructions produce codes that are either optimal with respect to the Johnson bound (J-optimal), or are asymptotically optimal and maximal. The constructions are based on certain pointsets in finite projective spaces of dimension k over GF(q) denoted PG(k,q)

n-Dimensional Optical Orthogonal Codes, Bounds and Optimal Constructions

We generalized to higher dimensions the notions of optical orthogonal codes. We establish uper bounds on the capacity of general $n$-dimensional OOCs, and on specific types of ideal codes (codes with zero off-peak autocorrelation). The bounds are based on the Johnson bound, and subsume many of the bounds that are typically applied to codes of dimension three or less. We also present two new constructions of ideal codes; one furnishes an infinite family of optimal codes for each dimension $n\ge 2$, and another which provides an asymptotically optimal family for each dimension $n\ge 2$. The constructions presented are based on certain point-sets in finite projective spaces of dimension $k$ over $GF(q)$ denoted $PG(k,q)$.Comment: 13 pages. arXiv admin note: text overlap with arXiv:1702.0645

Inhibiitorid ja fotoluminestsents-sondid proteiinkinaaside PKA ja PIM in vitro uuringuteks

Väitekirja elektrooniline versioon ei sisalda publikatsiooneProteiinkinaasid (PK-d) katalüüsivad valkude fosforüülimist. PK-de ebanormaalne aktiivsus rakkudes on korrelatsioonis keeruliste haigustega. Seetõttu teeb farmaatsiatööstus märkimisväärseid jõupingutusi, et reguleerida PK-de aktiivsust inhibiitoritega ja jälgida nende aktiivsust luminestsents-sondidega. Käesolevas töös kasutatud ARC-inhibiitorid on keemiliselt struktuurilt adenosiini matkivate heteroaromaatsete fragmentide ja peptiidide analoogide konjugaadid, neid ühendeid on pikemalt uuritud Tartu Ülikooli keemia instituudis. Käesolevas uuringus näidati, et PK PKA katalüütilise alaühiku α-isovormi (PKAcα) monoklonaalse antikeha (kloon D38C6) seondumine sihtvalguga on konkurentne ARC-Lum(Fluo) sondiga ja see antikeha inhibeerib substraadi fosforüülimist. Proovi järjestikust töötlemist nende konkureerivate PKAcα ligandidega kasutati tundliku AbARC immuunanalüüsi-meetodi väljatöötamiseks, mis võimaldas määrata väikseid koguseid (alates 93 pg) PKAcα rakulüsaatides. Hiljuti avastati Cushingi sündroomiga patsiendil S54L mutatsiooniga PRKACB geen. See mutatsioon viib PK glütsiinirikka aasa struktuuri muutumiseni. Käesolevas uuringus konstrueeriti muteerunud PK suhtes kuuekordse selektiivsusega inhibiitor. Lisaks töötati välja luminestsents-meetod PKAcβ-valgu kaubanduslike ja väljatöötatud inhibiitorite afiinsuse määramiseks. Koostöös Oxfordi ülikooliga viidi läbi ARC-inhibiitorite ja proteiinkinaasi PIM-1 komplekside röntgenstruktuuranalüüs. Saadud struktuurimudelitest lähtuvalt konstrueeriti lihtsustatud keemilise ehitusega ained. Uued inhibiitorid derivatiseeriti biotiiniga või fluorestsentsvärviga Cy5 ja neid aineid kasutati PIM-kinaasidetuvastamiseks biokeemilistes lahustes ja bioloogilistes proovides. Analüüsimeetod, milles kasutati ARC-sonde koos PIM-2-selektiivse antikehaga , võimaldas määrata sihtvalgu väikseid koguseid (alates 44 pg PIM-2). Konfokaalmikroskoopia abil tuvastati, et uued fluorestsents-sondid tungivad kiiresti U2OS-rakkudesse, kus nende paiknemine kattub PIM-1 ja fluorestsentsvalgu konjugaadi paiknemisega.Protein kinases (PKs) catalyze the phosphorylation of proteins. Abnormal activity of PKs in cells is correlated to complex diseases. Therefore, the pharma industry is making significant efforts to regulate the activity of PKs with inhibitors and to monitor the activity of PKs with luminescent probes. ARC inhibitors are conjugates of adenosine analogues and peptide mimetic moieties; they have been studied at length at the Institute of Chemistry of the University of Tartu. In the present study, it was shown that the binding of monoclonal antibody (clone D38C6) to α-isoform of the catalytic subunit of PKA (PKAcα) was competitive with binding of ARC-Lum(Fluo) probes. Sequential treatment of a sample with these competing PKAcα ligands was used to develop a sensitive AbARC immunoassay that allowed the determination of small amounts (from 93 pg) of PKAcα in cell lysates. Recently, PRKACB gene with the S54L mutation was discovered in a patient with the Cushing's syndrome. This mutation leads to a change in the structure of the glycine-rich loop of the PK. In the present study, an inhibitor with six-fold selectivity for the mutated PK was developed. In addition, a luminescence method was worked out for determination of affinity of both commercial and developed inhibitors of the PKAcβ protein. X-ray structure analysis of complexes of ARC inhibitors and PK PIM-1 was performed in collaboration with the University of Oxford. Based on the obtained structural models, compounds with simplified chemical structures were constructed. New inhibitors were derivatized with biotin or fluorescent dye Cy5 and applied for the detection of PIM PKs in biochemical solutions and complex biological samples. The sandwich assay utilizing a PIM-2-selective detection antibody featured a low limit of quantification (44 pg of PIM-2). A confocal microscopy study showed that the fluorescent probes were efficiently taken up by U2OS cells and the probes revealed high extent of co-localization with PIM-1-fused fluorescent proteins.https://www.ester.ee/record=b545989

Mechanisms coordinating peptidoglycan synthesis with the cell cycle in Staphylococcus aureus

"The emergence and spread of antibiotic resistance in bacteria constitutes one of the major challenges to global public health and is predicted to further escalate during the 21st century. One of the most frequent multi-drug resistant pathogens is methicillin-resistant Staphylococcus aureus (MRSA), a gram-positive coccoid bacterium that causes difficult to treat infections with severe morbidity and mortality rates. Many of the commonly used antibiotics target steps in the biosynthesis of peptidoglycan (PG), a robust but flexible meshlike macromolecule that withstands the intense internal turgor in the cell, among other functions. The integrity of the PG layer is of the utmost importance to bacteria, which must ensure that incorporation of new PG strands and remodelling of the existing ones is timely coordinated with the progression of the cell cycle. Despite its clinical relevance, many fundamental biological processes in S. aureus remain to be elucidated.(...)"

Advances in Topological Materials

The present collection of articles focuses on different aspects of topological-materials studies. Recent progress in both, theoretical and experimental, studies is covered in this Special Issue. A particular stress is given on different optical investigations, as well as on recent band-structure calculations. Besides, neutron scattering experiments, crystal growth, and a number of theoretical models for different topological systems are discussed

Active shape models with focus on overlapping problems applied to plant detection and soil pore analysis

[no abstract

Values of H_0 from Models of the Gravitational Lens 0957+561

The lensed double QSO 0957+561 has a well-measured time delay and hence is useful for a global determination of H0. Uncertainty in the mass distribution of the lens is the largest source of uncertainty in the derived H0. We investigate the range of \hn produced by a set of lens models intended to mimic the full range of astrophysically plausible mass distributions, using as constraints the numerous multiply-imaged sources which have been detected. We obtain the first adequate fit to all the observations, but only if we include effects from the galaxy cluster beyond a constant local magnification and shear. Both the lens galaxy and the surrounding cluster must depart from circular symmetry as well. Lens models which are consistent with observations to 95% CL indicate H0=104^{+31}_{-23}(1-\kthirty) km/s/Mpc. Previous weak lensing measurements constrain the mean mass density within 30" of G1 to be kthirty=0.26+/-0.16 (95% CL), implying H0=77^{+29}_{-24}km/s/Mpc (95% CL). The best-fitting models span the range 65--80 km/s/Mpc. Further observations will shrink the confidence interval for both the mass model and \kthirty. The range of H0 allowed by the full gamut of our lens models is substantially larger than that implied by limiting consideration to simple power law density profiles. We therefore caution against use of simple isothermal or power-law mass models in the derivation of H0 from other time-delay systems. High-S/N imaging of multiple or extended lensed features will greatly reduce the H0 uncertainties when fitting complex models to time-delay lenses.Comment: AASTEX, 48 pages 4 figures, 2 tables. Also available at: http://www.astro.lsa.umich.edu:80/users/philf/www/papers/list.htm

An Interdisciplinary Computational Study Of Magnetosphere-Ionsphere Coupling And Its Visual And Thermal Impact In The Auroral Region

Thesis (Ph.D.) University of Alaska Fairbanks, 2012A three-dimensional, three-fluid simulation (ions, electrons, and neutrals) was explicitly parallelized, facilitating the study of small-scale magnetospheric-ionospheric (M-I) coupling processes. The model has ionization and recombination, self-consistently (semi-empirically) determined collision frequencies, and a height resolved ionosphere. Inclusion of ion inertial terms in the momentum equation enables the propagation of Alfven waves. Investigation at small scales required large system domains, and thus fast parallel computers. The model was explicitly parallelized---enabling investigations of M-I coupling processes on very small temporal and spatial scales. The generation, reflection, and propagation of Alfven waves is of importance to the understanding of M-1 coupling processes---it is, in fact, the primary means of communication of physical processes in the coupled system. Alfvenic reflections were modeled for two different boundary conditions, and it was shown that the deformation of the current layer was Alfvenic in character. Visualizations of the data obtained appear to be consistent with the visual characteristics of actual discrete aurora in nature. The model reproduces qualitatively, and semi-quantitatively, in a self-consistent manner, some the behaviors of the formation and time-evolution of discrete arcs. These include the narrowness of arcs; electric fields extending parallel outward from the arcs; and fast (plasma) flows in the region of discrete arcs. Large-scale models---due to inevitable limitations of computational resources---need to make large-scale averages of computed properties. In regions of active small-scale structure, significant under-representation of the Joule heating occurs. It has been shown that the under-representation of the Joule heating in the region of active aurora can be as large as a factor of 8. This work includes a computer-based study of a quantitative approximation of this underrepresentation of the Joule heating by global, large-scale models and experimental observations